What are your favourite games that for whatever reason have been largely forgotten about or lost to time?

(Credit to big lantern ghost over on Famiboards for the thread topic)

The magical starsign/vacation series
There were only 2 games, magical vacation and its sequel, magical starsign.
I played starsign and it was my favorite JRPG of the early to mid DS days.

The games were made by "browny brown" known today as "1-up studio"

Totally agree. One of the most unique co-op experiences I've ever played, right there with Star Fox Zero. Too bad that with the dead of the Wii U and its Gamepad we won't see a game like ASA never again... 

To me... I think it has to be Wario Land: The Shake Dimension (Wario Land: Shake It! in the US). Not only the Land series has fallen into obscurity in favor of the Wario Ware series, but for the few people that still talks about Wario Land, Shake Dimension is too often forgotten. Which is insane, because to me its easily the best in the series. The platforming and puzzles are great, the level design is pretty original, it has far more content than any other Wario Land game and the visuals and music are fantastic. It's one of the Wii's little gems ^^

Twinsen's Odyssey
Arcanum

Does F-Zero GX count too? Forgotten by Nintendo at least...

Klonoa Series
Kirby Air Ride (City Trail Mode part of the game)
Dragonball Z: Bid for Power (Fanmade PC game if it counts)
Space Station: Silicon Valley
Samurai Jack (Gamecube)
Terranigma (I don't know if time has forgotten this treasure, but the reason why I put it on this list is because it's an amazing game that never got released in America but if it did, it would have had a renowned impact and would have been remembered in the same way as the likes Chrono Trigger & Secret of Mana did)

(Time has sorta forgotten these below to any young generations of gamers but but I'm sure they'll still be in the hearts of millions)
Worms
Lemmings

There will be more games that I can't think of atm.

Golden Sun series
Phantasy Star series
Shining Force series
Baten Kaitos
Turok series
Star Wars Shadows of the Empire (a personal fav, but probably not objectively a great game)
Mystical Ninja Starring Goemon / Goemon's Great Adventure
Wave Race 64 + GCN
Pilotwings
Ogre Battle Series
Shadowgate (NES + N64)
Lufia series (SNES, GBC, GBA)

... too many more for me to remember.

Yes, Lemmings definitely belongs on this list.  It was a bit before my time but I first played the PC version back in 1997 at a friend's place and instantly fell in love with it.  I know that it was super popular in the early 90's and was basically the original Angry Birds.  It's too bad that it is now largely forgotten.  Another great early PC game was the Even More Incredible Machine.

Skies of Arcadia

The first game that comes to my mind is Eternal Darkness on Gamecube. I would love if Nintendo resurrected this game and created a series.

Croc: Legend of the Gobbos. I’m not even gonna say it’s a good game, but I loved it and for whatever reason, it stuck with me to this very day! I love the character Croc and I still think about those fuzzy little orange bits and hope they’re all ok <3 (I should get out more…)

Vagrant story
Wing commader 4
Hogs of war